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- PDB-3hjl: The structure of full-length FliG from Aquifex aeolicus -

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Basic information

Entry
Database: PDB / ID: 3hjl
TitleThe structure of full-length FliG from Aquifex aeolicus
ComponentsFlagellar motor switch protein fliGFlagellar motor switch protein
KeywordsPROTON TRANSPORT / Armadillo repeat motif / superhelix / conformational plasticity / fold repeat / torque generation / bacterial flagellar motor / chemotaxis / rotary motor / switch complex / biological energy conversion / Bacterial flagellum / Cell inner membrane / Cell membrane / Flagellar rotation / Membrane
Function / homology
Function and homology information


bacterial-type flagellum basal body / cytoskeletal motor activity / bacterial-type flagellum-dependent cell motility / chemotaxis / plasma membrane
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2020 / Flagellar motor switch protein FliG, alpha-alpha superhelical domain / Flagellar motor switch protein FliG / Flagellar motor switch protein FliG, alpha-helical / Flagellar motor switch protein FliG, C-terminal / Flagellar motor switch protein FliG, N-terminal domain / Flagellar motor switch protein FliG, middle domain / FliG C-terminal domain / FliG middle domain / FliG N-terminal domain ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2020 / Flagellar motor switch protein FliG, alpha-alpha superhelical domain / Flagellar motor switch protein FliG / Flagellar motor switch protein FliG, alpha-helical / Flagellar motor switch protein FliG, C-terminal / Flagellar motor switch protein FliG, N-terminal domain / Flagellar motor switch protein FliG, middle domain / FliG C-terminal domain / FliG middle domain / FliG N-terminal domain / F-box domain / Annexin V; domain 1 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Flagellar motor switch protein FliG
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsLee, L.K. / Ginsburg, M.A. / Crovace, C. / Donohoe, M. / Stock, D.
CitationJournal: Nature / Year: 2010
Title: Structure of the torque ring of the flagellar motor and the molecular basis for rotational switching
Authors: Lee, L.K. / Ginsburg, M.A. / Crovace, C. / Donohoe, M. / Stock, D.
History
DepositionMay 22, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 4, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Flagellar motor switch protein fliG


Theoretical massNumber of molelcules
Total (without water)37,1411
Polymers37,1411
Non-polymers00
Water57632
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.997, 65.840, 67.791
Angle α, β, γ (deg.)90.000, 110.990, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Flagellar motor switch protein fliG / Flagellar motor switch protein


Mass: 37141.332 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: O66891
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.37 Å3/Da / Density % sol: 63.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.75
Details: 45% 1,4 butanediol, 0.1M Tris-Acetate, pH 8.75, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 25, 2006
RadiationMonochromator: Diamond (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.4→19.952 Å / Num. all: 19409 / Num. obs: 19157 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 57 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 10.4
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.322 / Mean I/σ(I) obs: 4.1 / Num. unique all: 2789 / % possible all: 99.9

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
MOSFLMdata reduction
SCALAdata scaling
SHELX& SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.4→19.952 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.917 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 17.096 / SU ML: 0.187 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.302 / ESU R Free: 0.249 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27 983 5.1 %RANDOM
Rwork0.216 ---
all0.219 19398 --
obs0.219 19153 98.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 102.59 Å2 / Biso mean: 64.411 Å2 / Biso min: 34.31 Å2
Baniso -1Baniso -2Baniso -3
1-2.56 Å20 Å23.35 Å2
2---0.3 Å20 Å2
3---0.14 Å2
Refinement stepCycle: LAST / Resolution: 2.4→19.952 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2535 0 0 32 2567
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222555
X-RAY DIFFRACTIONr_bond_other_d0.0020.021811
X-RAY DIFFRACTIONr_angle_refined_deg1.0652.0263429
X-RAY DIFFRACTIONr_angle_other_deg0.93934509
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.9875320
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.31126.952105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.83315561
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.8261511
X-RAY DIFFRACTIONr_chiral_restr0.0720.2417
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022712
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02399
X-RAY DIFFRACTIONr_nbd_refined0.1630.3573
X-RAY DIFFRACTIONr_nbd_other0.120.31737
X-RAY DIFFRACTIONr_nbtor_refined0.1470.51229
X-RAY DIFFRACTIONr_nbtor_other0.0850.51229
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0620.273
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1020.39
X-RAY DIFFRACTIONr_symmetry_vdw_other0.160.338
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0240.25
X-RAY DIFFRACTIONr_mcbond_it4.91441873
X-RAY DIFFRACTIONr_mcbond_other1.3634639
X-RAY DIFFRACTIONr_mcangle_it5.97262601
X-RAY DIFFRACTIONr_scbond_it5.27541006
X-RAY DIFFRACTIONr_scangle_it7.3736828
LS refinement shellResolution: 2.4→2.461 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 96 -
Rwork0.244 1285 -
all-1381 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
19.4925-2.165-4.44085.48141.73029.52230.0443-0.47430.0816-0.22180.2279-0.1015-0.37030.8653-0.2722-0.2188-0.0029-0.0385-0.13460.07380.0798-21.81283.031264.3545
22.8283-0.1765-1.42322.88151.04152.2285-0.0748-0.43780.01450.07430.13990.03860.08390.472-0.0651-0.28260.01670.0155-0.26310.0199-0.20384.665750.60569.5098
35.6173-0.5162-1.1268.0236-0.595712.3629-0.3471.06080.2582-1.35370.77690.4037-0.4637-1.6679-0.42990.0819-0.08480.00550.49170.2537-0.24364.425524.172136.3583
45.3066-0.7309-4.13224.29052.392515.5420.02740.1353-0.27230.23490.0252-0.08650.5633-1.0279-0.05260.1135-0.00860.0549-0.04460.0838-0.312324.624924.521922.5422
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 90
2X-RAY DIFFRACTION2A91 - 197
3X-RAY DIFFRACTION3A198 - 236
4X-RAY DIFFRACTION4A237 - 325

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